ISfinder

ISMch9

Family IS5
Group IS427

MGE type ISRelated element(s) :
Isoform Synonym(s)

Accession number	Transposition	Origin	Host
NC_011758	ND	Methylobacterium chloromethanicum	Methylobacterium chloromethanicum CM4

DNA section

IS Length : 848 bp

Ends

IR Length : 17/23

IRL : GAGCGTGGGACAAAACCGGTGTGAGCGGGTTGGAGGGTTATGGATGCTCT
IRR : GAGTCAGGGACAAAACCGTTTTGCCTGAGCTTGGCAGATGAGGGCGCAAG

Insertion site

Left flank	Direct repeat	Right flank	DR Length
ATCATGGGCC	TAA	GTTATGGACG	3

DNA sequence

GAGCGTGGGACAAAACCGGTGTGAGCGGGTTGGAGGGTTATGGATGCTCTCGTACCCGACGACCTTTGGGCGGTAGTCGAGCCGCTTCTGCCGCCTGAGC
CTGAGAAGCCGAAGGGCGGGCGACCGCGCGCCTCGGATCGGTCGGCGCTGGCCGGCATCATCTTGGTGCTGCGCACGGGCATGCAGTGGAAGCACCTGCC
ACATTCCGAGGTGGGCTGCAGCGGCAAGACGAGTTGGCGGCGGCTGGGCGCGTGGCAGGCGGCCGGCGTCTGGGCTGCACTGCATCGCGCGATGCTGGAG
CAGCTACAGGATGCCGGCGCGCTCGACTGGTCACGCGCTGCTCTCGACAGCGCCAGCTTGCCTGCGAAAAAAGGGGCGCCGCGACGGGCCCGAACCCAAC
GGATCGGGGCAAGCCGGGCACGAAGCGTCACCTCGTCGTGGACGCCAGAGGCACGCCGCTCGGCCTGACGCTCACGGGGGCCAACTGCCACGACAGCCGT
ATGCTGGCCGCCACGCTCGATGCCGTGCCAGGCGTGCGCACCGGCCGTCGTGGTCGCCCACGACGCAGACCCGACAAGCTGCACGCCGACAAGGGATACG
ATCATCACCGTTGCCGGTGCGAGTGCCGAGCCCGCCGCATCACCCCCCGGATCGCTCGGCGCGGCATCGAGAGCAGCGAGCGGCTGGGTCGTTACCGCTG
GATCGTCGAGCGAACGCTTGCCTGGCTGGCCCGCTTCCGCCGCCTCGCCATCCGCTACGAGCGGCGCGCTGACCTCCACCTCGCCTTCACCACGCTCGCT
TGCGCCCTCATCTGCCAAGCTCAGGCAAAACGGTTTTGTCCCTGACTC

Recoding section

Recoding by frameshift
Frame
Type
Experimentally demonstrated

Stimulators :

Shine-Dalgarno sequence :
Secondary structure :

Recoding motif :

Protein section

ORF number : 3

ORF 1

Length		Begin	End	Strand	Fusion ORF
429 bp	142 aa	40	468	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MDALVPDDLWAVVEPLLPPEPEKPKGGRPRASDRSALAGIILVLRTGMQWKHLPHSEVGCSGKTSWRRLGAWQAAGVWAALHRAMLEQLQDAGALDWSRA
ALDSASLPAKKGAPRRARTQRIGASRARSVTSSWTPEARRSA

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
519 bp	172 aa	327	845	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

LVTRCSRQRQLACEKRGAATGPNPTDRGKPGTKRHLVVDARGTPLGLTLTGANCHDSRMLAATLDAVPGVRTGRRGRPRRRPDKLHADKGYDHHRCRCEC
RARRITPRIARRGIESSERLGRYRWIVERTLAWLARFRRLAIRYERRADLHLAFTTLACALICQAQAKRFCP

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
806 bp	268 aa	40	845	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MDALVPDDLWAVVEPLLPPEPEKPKGGRPRASDRSALAGIILVLRTGMQWKHLPHSEVGCSGKTSWRRLGAWQAAGVWAALHRAMLEQLQDAGALDWSRA
ALDSASLPAKKRGAATGPNPTDRGKPGTKRHLVVDARGTPLGLTLTGANCHDSRMLAATLDAVPGVRTGRRGRPRRRPDKLHADKGYDHHRCRCECRARR
ITPRIARRGIESSERLGRYRWIVERTLAWLARFRRLAIRYERRADLHLAFTTLACALICQAQAKRFCP

Blast result :

Comments

ISMch9 is 92% aa similar to ISMdi24. The third ORF is the putative transposase reconstructed in silico by possible -1 frameshift.

References

1] Isfinder annotation (2010)
2] Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Chertkov,O., Brettin,T., Detter,J.C., Han,C., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Mikhailova,N., Marx,C. and Richardson,P. (2008) Direct submission GenBank.